Aquatic worms propagated in granular activated carbon (GAC) filter has become a troublesome problem for drinking water supply. This study investigated the vertical distribution patterns of naidids in GAC filter beds and assessed the effect of an additional sand bed, located below the GAC bed, in preventing naidids from being present in effluent. The results indicated that the vertical distribution data of naidids in the GAC filter bed were well fitted by a Gaussian distribution, and the location of peak population density was mainly affected by downward flow. Backwashing experiments revealed that additional pressure air scouring shifted the distribution pattern of naidids in the GAC filter bed, resulting in a significant enhancement in naidid removal efficiency. Additionally, the addition of a sand bed exhibited pronounced interception and inactivation effects on naidids, suggesting that it may be a very promising technology for preventing naidids propagated in GAC filters from being present in the effluent.